Differential display analysis on DNA and protein chips has proven useful in the identification of biomarkers for cancer. Isotope tagging methods, such as ICAT, have the potential to significantly improve the precision of these methods, but cannot currently be applied to protein chips where the tagged peptides cannot be effectively separated from untagged peptides. However, by incorporating one of the elements with atomic numbers between 35 (Br) and 63 (Eu) into isotopic tags, the resulting tagged peptides are shifted in the mass spectrum by 0.1 amu. As our preliminary work shows, these isotope differentiated binding energy shift tags (IDBEST) allow direct detection of the tagged peptides from untagged species in the mass spectrum without the need for affinity or liquid chromatography clean up of the sample. The goal of this project is to develop isotope differentiated binding energy shift tags (IDBEST) and associated mass spectral filtering algorithms that allow high precision (<10% standard deviation) differential display to be conducted directly on affinity protein chips.